Fact-checked by Grok 2 weeks ago

Nucleoside phosphoramidite

Nucleoside phosphoramidites are synthetic derivatives of natural or modified nucleosides, featuring a reactive phosphoramidite moiety at the 3'-hydroxyl position and various protecting groups to enable controlled chemical assembly of oligonucleotides.^[1] These compounds serve as the essential building blocks in the phosphoramidite method, the predominant technique for solid-phase synthesis of DNA and RNA sequences, allowing for the precise, stepwise addition of nucleotides in the 3' to 5' direction.^[2] First described in 1981 by Robert Beaucage and Marvin Caruthers, this chemistry revolutionized nucleic acid production by facilitating automated synthesis of custom oligonucleotides ranging from short primers to longer fragments up to approximately 200 bases.^[2]^[3] The core structure of a nucleoside phosphoramidite consists of a nucleobase (such as adenine, cytosine, guanine, thymine, or uracil), a ribose or deoxyribose sugar, and the phosphoramidite group, which is typically N,N-diisopropylamino or morpholino substituted for stability and reactivity.^[4] Protecting groups, including dimethoxytrityl (DMT) at the 5'-hydroxyl and acyl groups (e.g., benzoyl or isobutyryl) on the nucleobase, prevent unwanted side reactions during synthesis; for RNA phosphoramidites, additional protection at the 2'-position (e.g., tert-butyldimethylsilyl) is employed.^[1] The synthesis cycle involves detritylation to expose the 5'-OH, coupling with an activated phosphoramidite to form a phosphite triester, oxidation to a stable phosphate triester, and capping of unreacted sites, achieving coupling efficiencies typically exceeding 99%.^[2] Beyond standard oligonucleotide production, nucleoside phosphoramidites enable the incorporation of modifications such as fluorescent labels (e.g., Cy3 or Cy5), biotin, or non-natural bases, expanding their utility in applications like PCR primers, hybridization probes, gene synthesis, biosensors, and therapeutic oligonucleotides for diagnostics and drug development.^[4] This versatility has made phosphoramidite chemistry indispensable in molecular biology, structural studies, and biotechnology, with ongoing advancements in on-demand synthesis and modified analogs enhancing efficiency and scope.^[1]

Overview

Definition and General Structure

Nucleoside phosphoramidites are synthetic derivatives of natural or modified nucleosides, characterized by the attachment of a phosphoramidite group at either the 3' or 5' position of the sugar ring, serving as key intermediates in the solid-phase synthesis of oligonucleotides.^[5] These compounds enable the controlled assembly of DNA and RNA sequences by providing a reactive phosphorus(III) center that forms phosphite triester linkages during synthesis.^[6] The general molecular architecture features a heterocyclic nucleobase—such as adenine (A), cytosine (C), guanine (G), thymine (T) for DNA, or uracil (U) for RNA—glycosidically bonded to the 1' position of a five-membered furanose sugar, either β-D-2-deoxyribofuranose for DNA or β-D-ribofuranose for RNA. At the 3' position, the hydroxyl group is esterified with a phosphoramidite moiety, typically represented as -O-P(N(CH(CH₃)₂)₂)(OCH₂CH₂CN), where the diisopropylamino group acts as a leaving group and the 2-cyanoethyl serves as a protecting group. The 5' hydroxyl is protected, most commonly with a 4,4'-dimethoxytrityl (DMT) group, to allow selective deprotection during synthesis; for RNA phosphoramidites, an additional protecting group (e.g., tert-butyldimethylsilyl) is applied at the 2' position to prevent side reactions. The overall formula for a typical DNA building block is thus 5'-O-DMT-nucleoside-3'-O-(2-cyanoethyl N,N-diisopropylphosphoramidite), with base-specific protections (e.g., benzoyl for A and C, isobutyryl for G) to mask exocyclic amines.^[7]^[6]^[5] In oligonucleotide synthesis, the standard 3'-phosphoramidite configuration supports directional chain growth from the 3' to 5' end, where the activated 3' phosphoramidite couples to the free 5' hydroxyl of the resin-bound chain. In contrast, 5'-phosphoramidite variants, with the phosphoramidite at the 5' position and 3' protected or linked to a support, are employed for 5'-end modifications.^[5]^[8] These structural features ensure high efficiency in automated synthesizers, underpinning the production of custom nucleic acids for research and therapeutics.^[7]

Role in Nucleic Acid Chemistry

Nucleoside phosphoramidites emerged as pivotal building blocks in the 1980s, with their development by Serge L. Beaucage and Marvin H. Caruthers marking a transformative milestone in nucleic acid chemistry. In 1981, they introduced deoxynucleoside phosphoramidites as stable, reactive intermediates for solid-phase deoxypolynucleotide synthesis, enabling the efficient assembly of oligonucleotides through iterative coupling cycles.^[9] This innovation built on earlier phosphite-based approaches but addressed key limitations in stability and reactivity, facilitating the automation of synthesis processes that were previously labor-intensive.^[10] These compounds play a central role in generating custom DNA and RNA sequences essential for molecular biology and therapeutics. They are routinely used to synthesize short oligonucleotides such as PCR primers, fluorescent probes for hybridization assays, and antisense oligonucleotides that modulate gene expression by binding target mRNAs.^[10] In therapeutic contexts, phosphoramidite-derived sequences form the basis of FDA-approved drugs like fomivirsen and mipomersen, which target viral or disease-related nucleic acids.^[11] Compared to predecessor methods like the phosphotriester approach, the phosphoramidite method offers superior coupling efficiencies exceeding 98% per cycle, allowing scalable production of oligomers up to 200 nucleotides long with minimal truncation products.^[12] This high fidelity and compatibility with solid-phase automation have revolutionized fields beyond basic research, including gene synthesis for recombinant proteins and the production of guide RNAs for CRISPR-Cas9 genome editing.^[10] The method's impact extended dramatically during the COVID-19 pandemic, supporting the rapid development of mRNA vaccines through synthesis of modified nucleosides and capping structures that enhance stability and immunogenicity.^[13]

Chemical Properties

Phosphoramidite Moiety Characteristics

The phosphoramidite moiety features a trivalent phosphorus atom connected to two alkoxy groups—one typically linked to the 3'-hydroxyl of the nucleoside and the other to a β-cyanoethyl protecting group—and a dialkylamino substituent, most commonly diisopropylamino (N(iPr)₂), resulting in the general structure (RO)(R'O)P-NR₂ where R is the nucleoside residue and R' is the protecting group. This configuration imparts stability under neutral conditions while allowing selective activation for synthetic applications. The choice of diisopropylamino enhances solubility and reactivity compared to other amines, as originally demonstrated in the development of these compounds for polynucleotide assembly. Electronically, the phosphoramidite group exhibits a polarized P-N bond, with the lone pair on the nucleophilic nitrogen donating electrons to the phosphorus center, rendering the phosphorus electrophilic and prone to attack by nucleophiles such as alcohols in the presence of activators. This electronic imbalance facilitates the displacement of the amino group as a leaving group upon protonation, enabling efficient bond formation without harsh conditions. Such properties distinguish phosphoramidites from other phosphorus(III) derivatives, providing a balance of reactivity and handling ease essential for iterative chemical processes. Spectroscopically, the moiety is readily identified by its 31P NMR signal at approximately 150 ppm (ranging from 142 to 155 ppm depending on substituents), a value far downfield from the near 0 ppm typical of pentavalent phosphate esters, reflecting the P(III) oxidation state and coordination environment. This diagnostic shift aids in purity assessment and structural confirmation during preparation. Additionally, the group displays high sensitivity to moisture, rapidly hydrolyzing to the corresponding H-phosphonate (with a 31P NMR signal around 10-20 ppm) via nucleophilic addition of water to the electrophilic phosphorus, thereby requiring strictly anhydrous environments to prevent degradation and maintain synthetic efficacy.^[14]

Reactivity and Stability

Nucleoside phosphoramidites exhibit high reactivity in oligonucleotide synthesis through an activation mechanism involving protonation of the nitrogen atom in the phosphoramidite moiety by an acidic activator such as 1H-tetrazole. This protonation converts the neutral P(III) species into a reactive phosphonium-like intermediate, specifically a tetrazolylphosphane derivative, which facilitates nucleophilic attack by the 5'-hydroxyl group of the growing oligonucleotide chain.^[15] The coupling reaction proceeds via nucleophilic substitution at the phosphorus center, where the activated phosphoramidite reacts with the alcohol to form a phosphite triester linkage while displacing the protonated amine leaving group. A simplified representation of this process is:

(\ce{RO})_2\ce{P-NR2} + \ce{H+} \rightarrow [(\ce{RO})_2\ce{P^{+}-NHR2}] \xrightarrow{\ce{R'OH}} (\ce{RO})_2\ce{P-OR'} + \ce{HNR2}

This step achieves high efficiency, typically exceeding 98% yield per cycle under anhydrous conditions in acetonitrile solvent.^[15]^[7] As solids, nucleoside phosphoramidites demonstrate good stability to air oxidation and hydrolysis when stored as dry powders under an inert atmosphere at temperatures below 4°C, maintaining reactivity for extended periods. However, they decompose rapidly in protic solvents such as water or alcohols due to hydrolysis, which limits their shelf life to approximately 1-2 years under optimal anhydrous and inert storage conditions.^[16]^[17] Exposure to air or moisture can trigger side reactions, including oxidation to less reactive phosphate species and hydrolysis leading to H-phosphonate byproducts, which reduce coupling efficiency and introduce sequence errors in synthesis.^[16]^[18]

Synthesis

Preparation Methods

Nucleoside phosphoramidites are typically prepared from suitably protected nucleosides through a phosphitylation reaction at the 3'-hydroxyl group. The standard laboratory procedure begins with a 5'-O-(4,4'-dimethoxytrityl) (DMT)-protected nucleoside, where the exocyclic amino groups of adenine, guanine, and cytosine are also protected (e.g., with benzoyl groups) to prevent side reactions, while thymidine requires no base protection. This protected nucleoside is then reacted with 2-cyanoethyl N,N-diisopropylchlorophosphoramidite in an anhydrous solvent such as dichloromethane or tetrahydrofuran, in the presence of a base like N,N-diisopropylethylamine (DIPEA) or imidazole, under an inert atmosphere (e.g., argon) at room temperature for 1-2 hours. The reaction proceeds via nucleophilic displacement of the chloride by the 3'-OH, forming the P(III) phosphoramidite linkage with high regioselectivity due to the bulkier 5'-DMT group.^[7] Purification is achieved by silica gel column chromatography under argon to exclude moisture and oxygen, which can oxidize the sensitive P(III) center, followed by precipitation from hexane or pentane and filtration to yield the product as a white foam or powder stable under anhydrous conditions. Yields for this phosphitylation step are typically 80-95%, depending on the nucleobase and solvent purity.^[7] For RNA phosphoramidites, an additional 2'-O-protecting group is required to distinguish the 2'- and 3'-hydroxyls during synthesis; common choices include tert-butyldimethylsilyl (TBDMS), introduced prior to 5'-DMT protection using tert-butyldimethylsilyl chloride and imidazole in DMF, or the more labile (2-trityl-1,1-dimethylethyl)oxy methyl (TOM) group for easier deprotection. The subsequent 3'-phosphitylation follows the same protocol as for DNA analogs, with yields remaining in the 80-95% range, though TBDMS-protected uridine and guanosine may require optimized conditions to minimize 2'/3' migration.^[19] The foundational method was introduced by Beaucage and Caruthers in 1981, who synthesized deoxynucleoside phosphoramidites via reaction of protected 3'-hydroxyl nucleosides with bis(diisopropylamino)chlorophosphine (a P(III) chloride precursor) in the presence of DIPEA, followed by addition of 3-hydroxypropanenitrile to install the cyanoethyl group, enabling the first efficient solid-phase DNA synthesis. This two-step approach achieved good yields and established the phosphoramidite class as versatile intermediates.^[20]

Key Intermediates and Precursors

The primary precursors for nucleoside phosphoramidite production are protected nucleosides, such as 5'-O-(4,4'-dimethoxytrityl)-2'-deoxythymidine (5'-O-DMT-thymidine), where the 5'-hydroxyl group is shielded by a dimethoxytrityl (DMT) group to enable regioselective reaction at the 3'-hydroxyl, and phosphitylating agents like 2-cyanoethyl N,N-diisopropylchlorophosphoramidite, which introduce the reactive P(III) center with a cyanoethyl protecting group for subsequent oxidation.^[20]^[21] These precursors are derived from natural or synthetic nucleosides, with base protection (e.g., benzoyl for adenine and cytosine) applied to prevent side reactions during phosphitylation.^[21] Commercial suppliers of standard nucleoside phosphoramidites include Sigma-Aldrich and specialized vendors like Glen Research, which offer high-purity monomers for DNA and RNA synthesis, often in gram quantities suitable for laboratory use.^[22] For modified bases, such as 2'-fluoro derivatives used in therapeutic oligonucleotides, custom synthesis is common through these suppliers or contract manufacturers to accommodate specific sugar or base alterations.^[23] Key intermediates in the synthesis include dichlorophosphoramidites, such as N,N-diisopropylphosphorodichloridite derived from phosphorus trichloride (PCl3), which serve as P(III) sources and undergo selective amine displacement to form the diisopropylamino-phosphoramidite functionality before coupling to the nucleoside 3'-OH. This displacement step ensures the formation of the reactive P-N bond, with the intermediate purified to minimize oxidation-prone impurities. Purity requirements for these phosphoramidites and their precursors typically exceed 98% as determined by reverse-phase high-performance liquid chromatography (RP-HPLC), ensuring efficient coupling yields above 98% in downstream applications.^[24]^[25] Production scalability varies from laboratory-scale synthesis in grams using manual or semi-automated setups to industrial-scale in kilograms via continuous-flow or automated reactors, which optimize yield and reduce solvent use for cost-effective manufacturing of therapeutic-grade materials.^[26] Standard nucleoside phosphoramidites cost approximately $100–500 per gram at research scales, with economies of scale lowering prices for bulk industrial procurement.^[26]

Applications

Oligonucleotide Synthesis

Nucleoside phosphoramidites serve as the primary building blocks in the solid-phase phosphoramidite method for synthesizing oligonucleotides, enabling the automated assembly of DNA and RNA sequences in the 3' to 5' direction. This approach, pioneered in the early 1980s, relies on the high reactivity of the phosphoramidite group to form phosphite triester linkages that are subsequently oxidized to stable phosphate diesters. The method's efficiency stems from its cyclic nature, where each addition of a nucleotide monomer advances the chain by one unit, typically achieving stepwise yields of 95-99% for oligonucleotides ranging from 20 to 100 nucleotides in length.^[9]^[12] The synthesis cycle is performed on a solid support, such as controlled-pore glass (CPG) beads functionalized with the first nucleoside, allowing for easy washing and isolation of intermediates. The cycle comprises four sequential steps repeated for each nucleotide addition. First, detritylation removes the 5'-dimethoxytrityl (DMT) protecting group using an acid, such as trichloroacetic acid in dichloromethane, exposing the 5'-hydroxyl for the next reaction; this step typically takes 1-2 minutes and is monitored by the release of the orange DMT cation to assess efficiency. Second, coupling involves the addition of a 5'-protected nucleoside phosphoramidite monomer dissolved in acetonitrile, activated by a proton source like 1H-tetrazole, which protonates the nitrogen of the phosphoramidite to generate a reactive phosphonium intermediate that nucleophilically attacks the 5'-OH, forming a phosphite triester linkage in about 30 seconds to 5 minutes depending on the scale and modifier.^[7]^[27] Third, capping acetylates any unreacted 5'-OH groups with acetic anhydride and N-methylimidazole in tetrahydrofuran (THF) to prevent further elongation of truncated sequences, ensuring high purity and occurring in 1-2 minutes. Fourth, oxidation converts the unstable phosphite triester to a stable phosphate triester using iodine in water/THF or pyridine/water, a rapid step lasting about 1 minute that stabilizes the internucleotide linkage. Each full cycle, including washes with acetonitrile to remove byproducts, completes in approximately 5-10 minutes, allowing for the rapid synthesis of oligonucleotides up to 100 mers, with overall crude yields of full-length product typically 70-90% for short sequences (20-50 nt) and 20-50% for longer ones (up to 100 nt) at 99% stepwise efficiency, followed by purification to achieve high purity.^[27]^[7]^[2] The process is highly reactive under mild conditions, with the phosphoramidite's P(III) center facilitating nucleophilic attack while remaining stable during storage. Automation is standard using instruments like the Applied Biosystems (ABI) 394 synthesizer, which handles multiple columns simultaneously and delivers reagents via computer-controlled valves, using anhydrous solvents such as acetonitrile for coupling and THF for oxidation to minimize side reactions. These systems enable scalable production, from 10 nmol to 1 µmol scales, with built-in trityl monitoring to verify coupling success. Post-synthesis, the oligonucleotide is cleaved from the solid support and deprotected by treatment with concentrated aqueous ammonia at room temperature or elevated temperature for 1-24 hours, depending on the chemistry (DNA or RNA), which removes base and phosphate protecting groups while releasing the chain. The crude product is then purified by reverse-phase high-performance liquid chromatography (RP-HPLC) on C18 columns, eluting with acetonitrile gradients in aqueous buffers to isolate the full-length sequence, followed by desalting via ethanol precipitation or cartridge methods for final use. This workflow yields high-purity oligonucleotides suitable for molecular biology applications, with purification recovering 20-50% of the theoretical amount for longer sequences.^[28]^[27]^[29]

Specialized Uses and Modifications

Nucleoside phosphoramidites modified for phosphorothioate backbones incorporate sulfur atoms into the phosphate linkage, enhancing nuclease resistance in therapeutic oligonucleotides. This modification is achieved by sulfurizing the phosphite triester intermediate during solid-phase synthesis using agents like the Beaucage reagent (3H-1,2-benzodithiol-3-one 1,1-dioxide), which provides rapid and efficient sulfur transfer under mild conditions.^[30] Such phosphorothioate linkages are standard in antisense drugs, where they replace non-bridging oxygen atoms to improve stability without significantly altering hybridization properties.^[30] Locked nucleic acid (LNA) phosphoramidites feature a methylene bridge constraining the ribose ring into a C3'-endo conformation, increasing binding affinity to complementary nucleic acids by up to 10°C per modification and conferring high thermal stability.^[31] These are synthesized via standard phosphoramidite protocols and integrated into gapmer designs for RNase H-mediated cleavage in therapeutics targeting genes like Bcl-2 in cancer trials.^[31] Similarly, 2'-O-methoxyethyl (2'-MOE) phosphoramidites add an ethoxymethyl group at the 2' position of the ribose, boosting duplex stability, nuclease resistance, and low toxicity, making them ideal for steric-blocking oligonucleotides that modulate mRNA splicing in FDA-approved drugs.^[32] In advanced applications, these modified phosphoramidites enable the synthesis of aptamers, short single-stranded nucleic acids selected for high-affinity binding to targets like proteins or cells. Phosphoramidite chemistry facilitates post-selection modifications such as 2'-fluoro or phosphorodithioate substitutions, improving nuclease resistance and pharmacokinetics, as seen in pegaptanib for age-related macular degeneration.^[33] For small interfering RNAs (siRNAs), phosphoramidites with 2'-O-methyl or phosphorothioate modifications support the production of stable duplexes that trigger RNA interference; patisiran, approved by the FDA in 2018 for hereditary transthyretin-mediated amyloidosis, exemplifies this as the first lipid nanoparticle-delivered siRNA synthesized via automated phosphoramidite methods.^[34] More recent examples include imetelstat (approved 2024 for myelodysplastic syndromes) and olezarsen (approved 2024 for familial chylomicronemia syndrome), both featuring phosphorothioate modifications.^[35]^[36] Gene-editing guide RNAs for CRISPR-Cas systems are also chemically synthesized using phosphoramidites bearing 2'-O-methyl 3'-phosphorothioate caps at termini, significantly enhancing editing efficiency in primary human cells while reducing immune activation.^[37] Fluorescent and biotinylated nucleoside phosphoramidite analogs allow 5'-end labeling during synthesis, creating probes for detection assays. Biotin phosphoramidites incorporate biotin for streptavidin-based capture in microarrays, enabling high-throughput hybridization and signal amplification in diagnostic platforms. Fluorescent variants, such as those with Cy3 or Cy5 dyes, are used in fluorescence in situ hybridization (FISH) to visualize chromosomal loci with high specificity and minimal background.^[38] Emerging uses involve phosphoramidites for xeno nucleic acids (XNAs), synthetic polymers with alternative backbones like threose or arabinose sugars, advancing synthetic biology through expanded genetic codes and enzyme-resistant aptamers. Post-2015 developments include engineered polymerases for XNA amplification, enabling in vitro evolution of therapeutic candidates with unnatural base pairs for enhanced function and stability.^[39]

Protection and Deprotection Strategies

Protecting Group Selection

In nucleoside phosphoramidite synthesis, the exocyclic amino groups of adenine and cytosine are typically protected with benzoyl groups, while guanine employs an isobutyryl group; thymine and uracil require no such protection.^[2] These acyl protecting groups prevent side reactions, such as unwanted acylation or depurination, during the coupling steps of oligonucleotide assembly.^[40] For the ribose sugar moiety, the 5'-hydroxyl is commonly protected with a dimethoxytrityl (DMT) group, which enables selective detritylation at the 5'-end during solid-phase synthesis cycles.^[2] In RNA synthesis, the 2'-hydroxyl is protected with a tert-butyldimethylsilyl (TBDMS) group to enhance stability and prevent phosphitylation or migration to the reactive 3'-position.^[41] Key factors in selecting these protecting groups include orthogonality, where the acid-labile DMT is removed under mild acidic conditions without affecting the base-labile acyl groups on nucleobases, ensuring stepwise deprotection.^[42] Additional considerations are ease of installation and removal, as well as minimal risk of migration or steric hindrance that could impede coupling efficiency. The evolution of these strategies began with monomethoxytrityl (MMTr) and progressed to the more stable dimethoxytrityl (DMTr) in the early 1960s for 5'-protection, improving solubility and selectivity.^[43] By the late 1980s, ultra-mild groups like phenoxyacetyl (PAC) were introduced for adenine and guanine, offering faster ammonia deprotection suitable for sensitive therapeutic sequences while maintaining compatibility with standard phosphoramidite chemistry.^[44]

Deprotection Mechanisms

In oligonucleotide synthesis using nucleoside phosphoramidites, deprotection involves the removal of protecting groups from the assembled chain, typically occurring in two phases: stepwise removal during the synthesis cycle and global removal post-assembly. Stepwise deprotection primarily targets the 5'-dimethoxytrityl (DMT) group after each coupling step, achieved through acidic treatment with 3% trichloroacetic acid (TCA) in dichloromethane, which protonates the trityl ether and facilitates its departure as a stable carbocation, allowing monitoring via the released orange-colored DMT species.^[45] This process is rapid and quantitative under standard conditions, minimizing chain degradation while enabling iterative extension.^[7] Global deprotection follows cleavage from the solid support and addresses the base-protecting groups (e.g., benzoyl on adenine and cytosine, isobutyryl on guanine) and the cyanoethyl groups on the phosphate backbone. The conventional method employs concentrated aqueous ammonia (e.g., 28-30% NH₄OH) at 55°C for 8-16 hours, which simultaneously cleaves the oligonucleotide from the support and removes these groups, yielding the final phosphodiester-linked product.^[46] For base deprotection, the mechanism proceeds via nucleophilic acyl substitution, where ammonia attacks the carbonyl of the acyl protecting group, forming an amide intermediate that hydrolyzes to release the free nucleobase.^[2] In contrast, cyanoethyl removal from phosphorus occurs through β-elimination, initiated by deprotonation of the β-hydrogen under basic conditions, leading to extrusion of acrylonitrile and formation of the unprotected phosphate.^[47] This dual mechanism ensures efficient unmasking but generates byproducts like acrylonitrile, a known carcinogen.^[48] For RNA synthesis, an additional final deprotection step is required to remove the 2'-O-tert-butyldimethylsilyl (TBDMS) group, typically using triethylamine trihydrofluoride (TEA·3HF) or tetrabutylammonium fluoride (TBAF) in DMSO at 65°C for 2-3 hours, which cleaves the Si-O bond via nucleophilic attack by fluoride ion without affecting the phosphodiester backbone.^[49] Incomplete deprotection in these processes can result in persistent protecting groups, leading to impurities such as N-acylated bases or cyanoethyl-capped phosphates that compromise yield and purity, often necessitating additional purification like HPLC or PAGE.^[46] To address these challenges, especially for oligonucleotides with labile modifications, milder deprotection conditions have been developed, such as the ammonia-methylamine (AMA) mixture (1:1 v/v of 30% NH₄OH and 40% CH₃NH₂) at 65°C for 10 minutes, which accelerates base deprotection via enhanced nucleophilicity while reducing exposure time and byproduct formation.^[50] Gaseous methylamine under pressure offers an even faster alternative, completing deprotection in under 2 hours at room temperature for certain base-protected sequences.^[51] These methods, refined since the 1990s, preserve sensitive conjugates and have become standard for high-fidelity synthesis.^[44]

References

[1]
Phosphoramidite - an overview | ScienceDirect Topics
Reactive but noncritical phosphoramidite impurities are generated from nucleoside impurities with partially modified N, 5′-O or 2′-O (RNA)-protecting groups.
[2]
DNA Oligonucleotide Synthesis
### Summary of Introduction to Phosphoramidite Chemistry for DNA Oligonucleotide Synthesis
[3]
Phosphoramidite Chemistry for DNA and RNA Synthesis - BOC Sciences
### Summary of Phosphoramidite Chemistry for DNA and RNA Synthesis
[4]
Deoxynucleoside phosphoramidites—A new class of key ...
The development of a new class of nucleoside phosphites is described. These compounds are stable to normal laboratory conditions, are activated by mild acid ...
[5]
Phosphoramidite Chemistry for DNA Synthesis - Twist Bioscience
Phosphoramidites are modified nucleosides and are a standard chemical used in modern DNA synthesis. These molecules permit the sequential addition of new bases ...Missing: general formula
[6]
Nucleic Acids Book - Chapter 5: Solid-phase oligonucleotide synthesis
All oligonucleotides are made by phosphoramidite solid-phase synthesis. The steps in solid phase synthesis, and the preparation of reagents.Missing: formula | Show results with:formula
[7]
5' -> 3' Synthesis Phosphoramidites and Supports - Glen Research
Oligonucleotide synthesis typically proceeds from the 3' to 5' direction, mostly because the phosphoramidites for this direction are straight forward to ...Missing: formula | Show results with:formula
[8]
Deoxynucleoside phosphoramidites—A new class of key ...
The development of a new class of nucleoside phosphites is described. These compounds are stable to normal laboratory conditions, are activated by mild acid ...Missing: paper | Show results with:paper
[9]
Frontiers and Approaches to Chemical Synthesis of ... - NIH
Jan 15, 2013 · Reduced storage stability of synthons (Figure 4) and their solutions prevents the wide use of such phosphoramidites in the routine synthesis.
[10]
On-demand synthesis of phosphoramidites | Nature Communications
May 12, 2021 · All phosphoramidites showed more than 98% coupling yield and the four canonical nucleoside-phosphoramidites provided up to 99.8% coupling yield.
[11]
Oligonucleotide synthesis: Coupling efficiency and quality control | IDT
Nov 28, 2023 · Before oligonucleotide synthesis, each solid support is fixed with a phosphoramidite monomer—a chemically-modified DNA nucleotide (Figure 1).
[12]
mRNA medicine: Recent progresses in chemical modification ... - PMC
Sep 3, 2025 · Herein, we focus on recent progresses in three aspects of mRNA therapy: modification chemistry, sequence design and optimization, and structure ...3. Mrna Chemical... · 5. Mrna Engineering · 5.2. Circrna
[13]
Phosphoramidite compound identification and impurity control by ...
May 26, 2023 · The chemical structure of a phosphoramidite is shown in Figure 1. Each phosphoramidite is composed of a 5'-O-DMT sugar moiety (2 ...Missing: formula | Show results with:formula
[14]
Studies on the role of tetrazole in the activation of phosphoramidites
The mechanism of the tetrazole-activated coupling step in the synthesis of oligonucleotides via phosphoramidites is studied with the help of model reactions.Missing: intermediate | Show results with:intermediate
[15]
EP0061746A1 - Phosphoramidite compounds and their use in ...
The present new phosphoramidites are stable under normal laboratory conditions to hydrolysis and air oxidation, and are stored as dry, stable powders.Missing: shelf | Show results with:shelf
[16]
Phosphoramidous Acid - an overview | ScienceDirect Topics
Phosphoramidites tend to have long shelf lives when stored in the absence of air and under anhydrous conditions at temperatures below 4 °C.
[17]
[PDF] Guidebook for the Synthesis of Oligonucleotides
All phosphoramidites are susceptible to oxidation when left exposed to air and/or moisture. All phosphoramidites are stable in solution under argon for 2 ...
[18]
Nucleic Acids Book - Chapter 6: RNA oligonucleotide synthesis
The most common method of 2'-OH protection for RNA synthesis is the tert-butyldimethylsilyl (TBS) method. During synthesis of the phosphoramidite monomers, the ...
[19]
https://atdbio.com/nucleic-acids-book/RNA-oligonucleotide-synthesis
[20]
https://doi.org/10.1016/S0040-4039(01)90461-7
[21]
Natural DNA Phosphoramidites and Supports - Glen Research
Phosphoramidites and supports for DNA synthesis are produced to ensure the highest performance on commercial oligonucleotide synthesizers. Learn more!
[22]
2'-F-RNA Phosphoramidites | Glen Research
Glen Research 2'-F-RNA Phosphoramidites are produced and packaged to ensure the highest performance on commercial synthesizers. Learn more!
[23]
Phosphoramidites | Fisher Scientific
HPLC Purity—≥98.0%• 31P NMR Purity—≥98.0%; Sum of PIII impurities (141-152ppm) ≤ 0.5%For Research Use Only. Not for use in diagnostic procedures.
[24]
[PDF] Quality Standards for DNA phosphoramidite raw materials
The phosphoramidite moiety consists of two groups: a diisopropylamino group which is removed during synthesis and links the phosphoramidites to the growing.Missing: definition | Show results with:definition
[25]
Comprehensive Statistical Analysis of Phosphoramidites - AxisPharm
Sep 18, 2024 · Phosphoramidites are key reagents in the synthesis of oligonucleotides, including DNA, RNA, and their analogs. These compounds, derived from ...2. Global Market Overview · Spacer And Linker... · Locked Nucleic Acid (lna)...Missing: nucleoside | Show results with:nucleoside<|control11|><|separator|>
[26]
Standard Protocol for Solid-Phase Oligonucleotide Synthesis using ...
The Synthesis Cycle · Deblocking · Activation & Coupling · Capping · Oxidation · Cleavage & Deprotection · DMT ON Synthesis · Storage & Stability.
[27]
DNA/RNA Synthesizer Model 394
This machine is an automated DNA/RNA synthesizer, Model 394 from Applied Biosystems, Inc. It was on the market from 1991 to 2007.
[28]
Protocol for the Solid-phase Synthesis of Oligomers of RNA ... - NIH
Jul 28, 2017 · 1. Solid-phase Synthesis of RNA Oligonucleotides · Preparation of solutions containing each phosphoramidite (Table 1). · Set-up of sequence and ...
[29]
Synthesis of oligodeoxyribonucleoside phosphorothioates using ...
Among these compounds, the Beaucage reagent is widely used because of its rapid sulfur transfer reaction rate and commercial availability. However, this reagent ...
[30]
Locked nucleic acid (LNA): High affinity targeting of RNA for ...
Locked nucleic acid (LNA) is a nucleic acid analogue containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA mimicking ...
[31]
Chemical Modifications of Nucleic Acid Aptamers for Therapeutic ...
Aug 2, 2017 · DNA aptamers can be synthesized through the classic solid phase phosphoramidite four-step process on the automated DNA synthesizer [18]. The ...
[32]
Page Not Found | FDA
No readable text found in the HTML.<|control11|><|separator|>
[33]
Chemically modified guide RNAs enhance CRISPR-Cas genome ...
Jun 29, 2015 · Streamlined process for the chemical synthesis of RNA using 2′-O-thionocarbamate-protected nucleoside phosphoramidites in the solid phase. J ...
[34]
Freedom dyes - Fluorescein, ATTO, Rhodamine, CY | IDT
Cy 5.5 can also be used to label DNA oligos for use as hybridization probes in other applications, such as fluorescent in situ hybridization (FISH). Freedom ...
[35]
Modified nucleic acids: replication, evolution, and next-generation ...
Sep 2, 2020 · Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the ...
[36]
https://www.accessdata.fda.gov/drugsatfda_docs/appletter/2024/218614Orig1s000ltr.pdf
[37]
Standard RNA Phosphoramidites and Supports - Glen Research
TOM-Protected RNA monomers are also fully compatible with minor bases with 2'-O-TBDMS protection. TBDMS-Protected RNA Phosphoramidites. Glen Research CE (ß ...
[38]
5′-DMT-protected double-stranded DNA - ScienceDirect.com
Mar 15, 2021 · During ON synthesis orthogonal protection systems must be used, most of which are based on acid-labile 4,4ʹ-dimethoxytrityl (DMT) protective ...
[39]
https://pmc.ncbi.nlm.nih.gov/articles/PMC7469316/
[40]
Kinetic Studies on Depurination and Detritylation of CPG-Bound ...
For example, use of the strongly acidic TCA leads to significant depurination, while use of less acidic DCA may lead to incomplete detritylation (<98–99%).Results And Discussion · Dimer Depurination · Detritylation Kinetics
[41]
Advanced method for oligonucleotide deprotection - PMC - NIH
It involves the sequential assembling of nucleotides on an insoluble solid support, cleavage of the synthesized oligonucleotides from the support, removal of ...
[42]
Synthesis of Oligodeoxynucleotides Using Fully Protected ...
The phosphitylation of 3 with bis(diisopropylamino)(2-cyanoethoxy)phosphine produced the fully protected phosphoramidite unit 4 in 73% yield (Scheme 1).
[43]
WO2000046231A1 - Method for deprotecting oligonucleotides
Under these conditions, 2-cyanoethyl group undergoes β-elimination with the release of acrylonitrile. Acrylonitrile has shown to be a potent carcinogen ...
[44]
Safe deprotection strategy for the tert-butyldimethylsilyl (TBS) group ...
Desilylation using ammonium fluoride is applicable to fully protected "RNA only" substrates and desilylation using potassium fluoride is applicable to "mixed ...
[45]
Cleavage of Oligodeoxyribonucleotides from Controlled-Pore Glass ...
A novel method for the deprotection of oligodeoxyribonucleotides has been developed. Gaseous amines such as ammonia or methylamine were employed under pressure.
[46]
The use of gaseous ammonia for the deprotection and cleavage ...
The use of ammonia gas under pressure provides a convenient procedure for the deprotection of oligonucleotides, and analogs synthesized using N-pent-4-enoyl ...Missing: mechanism | Show results with:mechanism
[47]
The final deprotection step in oligonucleotide synthesis is reduced to ...
The final deprotection step in oligonucleotide synthesis is reduced to a mild and rapid ammonia treatment by using labile base-protecting groups Open Access.